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Genomic regulation of pork quality was investigated using loins (n = 4,025) which were evaluated during large-scale industrial research projects (n = 4) in which loins were evaluated between 2009 and 2016. Additionally, biceps femoris samples from pigs (n = 1,019) harvested by a commercial seedstock supplier were used to study the genetic regulation of a ham muscle color defect referred to as ham halo. Strong genetic regulation of fatty acid profile was observed for HIF1AN and SCD, which are two genes located on Chromosome 14. Variation in these two genes impacted the proportion of saturated fatty acids. Specifically, the proportion of stearic acid was strongly influenced by variation in these two genes. Selection for animals more prone to produce saturated fatty should result in improved bacon/belly quality. Given the negative effects that feeding high levels of ingredients that contain a high level of polyunsaturated fatty acids has on fat quality, the ability to genetic select for greater propensity to deposit more saturated fat should help reduce the impact of using those feed ingredients. Additionally, a region on Chromosome X was identified that impacts the proportion of polyunsaturated fatty acids.

Genetic variation on chromosome 15, in the region where Protein Kinase AMP-Activated Non-Catalytic Subunit Gamma 3 (PRKAG3) is located, was a strong regulator of ultimate pH of the loin muscle in this study, as has been shown in numerous other studies. The genomic analysis of loins sampled in 2015 and 2016 for the NPB Instrument Grading Project showed the allelic frequency of the favorable (higher ultimate pH) to be 0.72. Thus, it appears that the industry needs to continue/intensify selection pressure on PRKAG3 to optimize ultimate pH and water-holding capacity. Simultaneous selection for favorable forms of PRKAG3. and calpastatin (CAST) should allow the industry produce loins that will be tender and juicy even if the consumer over cooks the product.
Contact: Dr. Steven Shackelford, USDA-ARS U.S. Meat Animal Research Center, steven.shackelford@ars.usda.gov, 402-762-4223.